Starting phenix.real_space_refine on Wed Mar 12 23:59:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zl1_60215/03_2025/8zl1_60215.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zl1_60215/03_2025/8zl1_60215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zl1_60215/03_2025/8zl1_60215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zl1_60215/03_2025/8zl1_60215.map" model { file = "/net/cci-nas-00/data/ceres_data/8zl1_60215/03_2025/8zl1_60215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zl1_60215/03_2025/8zl1_60215.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 88 5.16 5 C 5624 2.51 5 N 1328 2.21 5 O 1424 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8466 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4183 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 505} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 4183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4183 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 33, 'TRANS': 505} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.49, per 1000 atoms: 0.65 Number of scatterers: 8466 At special positions: 0 Unit cell: (86.7825, 97.527, 105.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 88 16.00 P 2 15.00 O 1424 8.00 N 1328 7.00 C 5624 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.23 Conformation dependent library (CDL) restraints added in 964.4 milliseconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2012 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 0 sheets defined 80.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 33 through 60 removed outlier: 3.629A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N LYS A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N GLY A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) Proline residue: A 50 - end of helix Proline residue: A 55 - end of helix removed outlier: 3.654A pdb=" N ASN A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 81 Processing helix chain 'A' and resid 84 through 100 removed outlier: 3.757A pdb=" N ILE A 91 " --> pdb=" O VAL A 87 " (cutoff:3.500A) Proline residue: A 92 - end of helix Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.659A pdb=" N TYR A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 132 removed outlier: 3.554A pdb=" N CYS A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.624A pdb=" N ARG A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 166 Processing helix chain 'A' and resid 169 through 191 Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 220 through 238 Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.643A pdb=" N LEU A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 295 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 301 through 313 removed outlier: 3.789A pdb=" N GLU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 329 Processing helix chain 'A' and resid 333 through 352 Processing helix chain 'A' and resid 372 through 386 removed outlier: 4.398A pdb=" N THR A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 392 No H-bonds generated for 'chain 'A' and resid 390 through 392' Processing helix chain 'A' and resid 393 through 398 Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 423 through 442 removed outlier: 4.238A pdb=" N PHE A 427 " --> pdb=" O TRP A 423 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY A 432 " --> pdb=" O LEU A 428 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 452 Processing helix chain 'A' and resid 453 through 458 removed outlier: 4.081A pdb=" N VAL A 457 " --> pdb=" O GLY A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 476 Processing helix chain 'A' and resid 479 through 498 Proline residue: A 489 - end of helix Processing helix chain 'A' and resid 501 through 513 removed outlier: 3.865A pdb=" N LEU A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 523 through 533 Processing helix chain 'A' and resid 536 through 544 Processing helix chain 'A' and resid 544 through 567 removed outlier: 4.926A pdb=" N LEU A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'B' and resid 34 through 40 Processing helix chain 'B' and resid 40 through 59 Proline residue: B 50 - end of helix Proline residue: B 55 - end of helix Processing helix chain 'B' and resid 62 through 81 removed outlier: 3.649A pdb=" N ARG B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 90 through 100 removed outlier: 4.095A pdb=" N VAL B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) Proline residue: B 97 - end of helix Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.592A pdb=" N TYR B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 132 removed outlier: 3.501A pdb=" N CYS B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 removed outlier: 3.609A pdb=" N ARG B 137 " --> pdb=" O ASN B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 166 Processing helix chain 'B' and resid 169 through 191 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 220 through 238 Processing helix chain 'B' and resid 239 through 240 No H-bonds generated for 'chain 'B' and resid 239 through 240' Processing helix chain 'B' and resid 241 through 244 Processing helix chain 'B' and resid 245 through 259 removed outlier: 3.661A pdb=" N LEU B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 296 Proline residue: B 277 - end of helix Processing helix chain 'B' and resid 304 through 314 Processing helix chain 'B' and resid 316 through 329 Processing helix chain 'B' and resid 333 through 352 Processing helix chain 'B' and resid 372 through 386 removed outlier: 3.960A pdb=" N THR B 376 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 392 No H-bonds generated for 'chain 'B' and resid 390 through 392' Processing helix chain 'B' and resid 393 through 398 Processing helix chain 'B' and resid 413 through 421 Processing helix chain 'B' and resid 423 through 442 removed outlier: 4.222A pdb=" N PHE B 427 " --> pdb=" O TRP B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 454 removed outlier: 4.224A pdb=" N GLY B 454 " --> pdb=" O ASN B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 455 through 458 Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 479 through 498 Proline residue: B 489 - end of helix Processing helix chain 'B' and resid 501 through 513 removed outlier: 3.970A pdb=" N LEU B 505 " --> pdb=" O HIS B 501 " (cutoff:3.500A) Proline residue: B 508 - end of helix Processing helix chain 'B' and resid 523 through 533 Processing helix chain 'B' and resid 536 through 567 removed outlier: 3.507A pdb=" N MET B 540 " --> pdb=" O ARG B 536 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY B 546 " --> pdb=" O ILE B 542 " (cutoff:3.500A) Proline residue: B 547 - end of helix removed outlier: 4.757A pdb=" N LEU B 564 " --> pdb=" O GLN B 560 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 565 " --> pdb=" O THR B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 584 562 hydrogen bonds defined for protein. 1674 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 2.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1297 1.32 - 1.44: 2274 1.44 - 1.57: 4967 1.57 - 1.69: 4 1.69 - 1.81: 146 Bond restraints: 8688 Sorted by residual: bond pdb=" N SER B 302 " pdb=" CA SER B 302 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.23e-02 6.61e+03 7.65e+00 bond pdb=" N VAL B 308 " pdb=" CA VAL B 308 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.58e+00 bond pdb=" N MET B 295 " pdb=" CA MET B 295 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.26e-02 6.30e+03 7.31e+00 bond pdb=" N LYS A 260 " pdb=" CA LYS A 260 " ideal model delta sigma weight residual 1.454 1.485 -0.031 1.23e-02 6.61e+03 6.41e+00 bond pdb=" N GLU B 307 " pdb=" CA GLU B 307 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.23e-02 6.61e+03 5.87e+00 ... (remaining 8683 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.33: 11616 2.33 - 4.66: 168 4.66 - 6.99: 24 6.99 - 9.32: 1 9.32 - 11.65: 1 Bond angle restraints: 11810 Sorted by residual: angle pdb=" N GLU B 304 " pdb=" CA GLU B 304 " pdb=" C GLU B 304 " ideal model delta sigma weight residual 113.30 107.06 6.24 1.34e+00 5.57e-01 2.17e+01 angle pdb=" O11 PTY B 601 " pdb=" P1 PTY B 601 " pdb=" O14 PTY B 601 " ideal model delta sigma weight residual 92.90 104.55 -11.65 3.00e+00 1.11e-01 1.51e+01 angle pdb=" CA SER B 302 " pdb=" C SER B 302 " pdb=" O SER B 302 " ideal model delta sigma weight residual 121.23 117.13 4.10 1.07e+00 8.73e-01 1.47e+01 angle pdb=" N GLN B 309 " pdb=" CA GLN B 309 " pdb=" C GLN B 309 " ideal model delta sigma weight residual 110.97 107.09 3.88 1.09e+00 8.42e-01 1.27e+01 angle pdb=" CA LYS A 260 " pdb=" C LYS A 260 " pdb=" O LYS A 260 " ideal model delta sigma weight residual 121.46 117.34 4.12 1.17e+00 7.31e-01 1.24e+01 ... (remaining 11805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.01: 4971 26.01 - 52.02: 166 52.02 - 78.04: 9 78.04 - 104.05: 0 104.05 - 130.06: 4 Dihedral angle restraints: 5150 sinusoidal: 2026 harmonic: 3124 Sorted by residual: dihedral pdb=" CA ARG A 371 " pdb=" C ARG A 371 " pdb=" N ASN A 372 " pdb=" CA ASN A 372 " ideal model delta harmonic sigma weight residual 180.00 152.55 27.45 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" N1 PTY B 601 " pdb=" C2 PTY B 601 " pdb=" C3 PTY B 601 " pdb=" O11 PTY B 601 " ideal model delta sinusoidal sigma weight residual 65.33 -64.73 130.06 1 3.00e+01 1.11e-03 1.75e+01 dihedral pdb=" C3 PTY A 601 " pdb=" O11 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O12 PTY A 601 " ideal model delta sinusoidal sigma weight residual 300.23 176.96 123.27 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 5147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1072 0.052 - 0.104: 263 0.104 - 0.155: 32 0.155 - 0.207: 8 0.207 - 0.259: 1 Chirality restraints: 1376 Sorted by residual: chirality pdb=" C6 PTY B 601 " pdb=" C1 PTY B 601 " pdb=" C5 PTY B 601 " pdb=" O7 PTY B 601 " both_signs ideal model delta sigma weight residual False 2.49 2.23 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA LYS A 260 " pdb=" N LYS A 260 " pdb=" C LYS A 260 " pdb=" CB LYS A 260 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.12e-01 chirality pdb=" CA VAL B 308 " pdb=" N VAL B 308 " pdb=" C VAL B 308 " pdb=" CB VAL B 308 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.01e-01 ... (remaining 1373 not shown) Planarity restraints: 1440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS A 559 " 0.012 2.00e-02 2.50e+03 2.34e-02 5.47e+00 pdb=" C CYS A 559 " -0.040 2.00e-02 2.50e+03 pdb=" O CYS A 559 " 0.015 2.00e-02 2.50e+03 pdb=" N GLN A 560 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 559 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.56e+00 pdb=" C CYS B 559 " -0.037 2.00e-02 2.50e+03 pdb=" O CYS B 559 " 0.014 2.00e-02 2.50e+03 pdb=" N GLN B 560 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 54 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO B 55 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 55 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 55 " 0.029 5.00e-02 4.00e+02 ... (remaining 1437 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1118 2.75 - 3.29: 8911 3.29 - 3.83: 14599 3.83 - 4.36: 16814 4.36 - 4.90: 29014 Nonbonded interactions: 70456 Sorted by model distance: nonbonded pdb=" O MET B 279 " pdb=" OG1 THR B 283 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR A 350 " pdb=" OG1 THR A 376 " model vdw 2.244 3.040 nonbonded pdb=" O VAL A 348 " pdb=" OG1 THR A 352 " model vdw 2.323 3.040 nonbonded pdb=" OG SER A 373 " pdb=" OG SER B 104 " model vdw 2.329 3.040 nonbonded pdb=" OG1 THR B 475 " pdb=" OD1 ASN B 480 " model vdw 2.340 3.040 ... (remaining 70451 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 22.130 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8688 Z= 0.270 Angle : 0.653 11.651 11810 Z= 0.366 Chirality : 0.044 0.259 1376 Planarity : 0.005 0.052 1440 Dihedral : 12.593 130.060 3138 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.22 % Allowed : 0.11 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1070 helix: 1.41 (0.18), residues: 792 sheet: None (None), residues: 0 loop : -0.71 (0.36), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 414 HIS 0.003 0.001 HIS A 135 PHE 0.020 0.001 PHE A 251 TYR 0.027 0.001 TYR B 111 ARG 0.010 0.001 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.910 Fit side-chains REVERT: A 323 ASP cc_start: 0.9217 (t70) cc_final: 0.8827 (p0) REVERT: A 340 MET cc_start: 0.9323 (ttm) cc_final: 0.9080 (ttm) REVERT: A 349 MET cc_start: 0.9171 (mmm) cc_final: 0.8869 (mmm) REVERT: B 267 ASP cc_start: 0.8221 (t0) cc_final: 0.7944 (t0) REVERT: B 363 ASP cc_start: 0.9073 (m-30) cc_final: 0.8855 (m-30) outliers start: 2 outliers final: 0 residues processed: 80 average time/residue: 1.4596 time to fit residues: 124.1795 Evaluate side-chains 69 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 0.0270 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.1980 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 overall best weight: 1.0444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN B 189 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.065578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.050373 restraints weight = 27087.367| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.28 r_work: 0.2738 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8688 Z= 0.182 Angle : 0.564 6.730 11810 Z= 0.291 Chirality : 0.041 0.162 1376 Planarity : 0.005 0.047 1440 Dihedral : 8.380 113.058 1226 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.88 % Allowed : 5.51 % Favored : 93.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.25), residues: 1070 helix: 1.40 (0.18), residues: 824 sheet: None (None), residues: 0 loop : -0.94 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 414 HIS 0.002 0.001 HIS A 135 PHE 0.026 0.001 PHE A 251 TYR 0.034 0.001 TYR A 282 ARG 0.008 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.977 Fit side-chains REVERT: A 323 ASP cc_start: 0.9319 (t70) cc_final: 0.8899 (p0) REVERT: A 332 MET cc_start: 0.8107 (ttm) cc_final: 0.7748 (ttp) REVERT: A 340 MET cc_start: 0.9272 (ttm) cc_final: 0.9054 (ttm) REVERT: A 349 MET cc_start: 0.9285 (mmm) cc_final: 0.8953 (mmm) REVERT: B 267 ASP cc_start: 0.8160 (t0) cc_final: 0.7871 (t0) REVERT: B 363 ASP cc_start: 0.9137 (m-30) cc_final: 0.8902 (m-30) outliers start: 8 outliers final: 2 residues processed: 77 average time/residue: 1.3562 time to fit residues: 111.3420 Evaluate side-chains 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 MET Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 57 optimal weight: 3.9990 chunk 78 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 29 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 49 optimal weight: 7.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 GLN A 372 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.064880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.049517 restraints weight = 27428.905| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.31 r_work: 0.2706 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8688 Z= 0.255 Angle : 0.578 6.889 11810 Z= 0.293 Chirality : 0.041 0.174 1376 Planarity : 0.005 0.046 1440 Dihedral : 8.095 124.748 1226 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.32 % Allowed : 7.60 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1070 helix: 1.48 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.12 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 414 HIS 0.005 0.001 HIS A 335 PHE 0.025 0.001 PHE A 251 TYR 0.028 0.001 TYR A 282 ARG 0.004 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 323 ASP cc_start: 0.9323 (t70) cc_final: 0.8906 (p0) REVERT: A 332 MET cc_start: 0.8041 (ttm) cc_final: 0.7784 (ttp) REVERT: A 349 MET cc_start: 0.9295 (mmm) cc_final: 0.8961 (mmm) REVERT: B 267 ASP cc_start: 0.8168 (t0) cc_final: 0.7878 (t0) outliers start: 12 outliers final: 5 residues processed: 75 average time/residue: 1.3422 time to fit residues: 107.4896 Evaluate side-chains 79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 323 ASP Chi-restraints excluded: chain B residue 494 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 94 optimal weight: 8.9990 chunk 89 optimal weight: 0.4980 chunk 93 optimal weight: 0.6980 chunk 104 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 372 ASN B 480 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.066025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.050663 restraints weight = 27082.630| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.30 r_work: 0.2740 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8688 Z= 0.167 Angle : 0.540 6.949 11810 Z= 0.276 Chirality : 0.040 0.162 1376 Planarity : 0.005 0.045 1440 Dihedral : 7.824 125.558 1226 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.10 % Allowed : 9.03 % Favored : 89.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.25), residues: 1070 helix: 1.55 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.10 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 414 HIS 0.003 0.001 HIS A 135 PHE 0.022 0.001 PHE A 251 TYR 0.026 0.001 TYR A 282 ARG 0.003 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.989 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.9309 (t70) cc_final: 0.8900 (p0) REVERT: A 349 MET cc_start: 0.9333 (mmm) cc_final: 0.8968 (mmm) REVERT: B 267 ASP cc_start: 0.8158 (t0) cc_final: 0.7856 (t0) outliers start: 10 outliers final: 2 residues processed: 76 average time/residue: 1.3424 time to fit residues: 108.8510 Evaluate side-chains 75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 73 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 374 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 79 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN A 389 ASN B 106 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.064577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.049167 restraints weight = 27407.195| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 3.31 r_work: 0.2700 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8688 Z= 0.282 Angle : 0.572 7.284 11810 Z= 0.291 Chirality : 0.041 0.173 1376 Planarity : 0.005 0.045 1440 Dihedral : 7.962 125.206 1226 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.32 % Allowed : 10.35 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.25), residues: 1070 helix: 1.54 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.16 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 414 HIS 0.005 0.001 HIS A 335 PHE 0.023 0.001 PHE A 251 TYR 0.024 0.001 TYR A 282 ARG 0.002 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.887 Fit side-chains REVERT: A 323 ASP cc_start: 0.9297 (t70) cc_final: 0.8915 (p0) REVERT: A 349 MET cc_start: 0.9337 (mmm) cc_final: 0.8971 (mmm) REVERT: B 267 ASP cc_start: 0.8199 (t0) cc_final: 0.7905 (t0) outliers start: 12 outliers final: 4 residues processed: 80 average time/residue: 1.2987 time to fit residues: 111.2775 Evaluate side-chains 75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 2 optimal weight: 0.0670 chunk 81 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 26 optimal weight: 7.9990 chunk 34 optimal weight: 4.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.066091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.050861 restraints weight = 26875.988| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.28 r_work: 0.2745 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8688 Z= 0.161 Angle : 0.535 8.851 11810 Z= 0.273 Chirality : 0.040 0.160 1376 Planarity : 0.005 0.044 1440 Dihedral : 7.778 122.012 1226 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.88 % Allowed : 11.67 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1070 helix: 1.57 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.12 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 414 HIS 0.002 0.001 HIS A 135 PHE 0.019 0.001 PHE A 251 TYR 0.025 0.001 TYR A 282 ARG 0.003 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.914 Fit side-chains REVERT: A 323 ASP cc_start: 0.9295 (t70) cc_final: 0.8928 (p0) REVERT: A 349 MET cc_start: 0.9367 (mmm) cc_final: 0.9000 (mmm) REVERT: B 267 ASP cc_start: 0.8258 (t0) cc_final: 0.7980 (t0) REVERT: B 312 ARG cc_start: 0.7642 (mmt180) cc_final: 0.7229 (mmp80) outliers start: 8 outliers final: 4 residues processed: 76 average time/residue: 1.3087 time to fit residues: 106.3996 Evaluate side-chains 76 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 68 MET Chi-restraints excluded: chain B residue 176 MET Chi-restraints excluded: chain B residue 220 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.0040 chunk 10 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.066788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.051567 restraints weight = 26981.606| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.31 r_work: 0.2766 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8688 Z= 0.153 Angle : 0.517 9.395 11810 Z= 0.264 Chirality : 0.039 0.156 1376 Planarity : 0.005 0.044 1440 Dihedral : 7.476 114.478 1226 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.10 % Allowed : 12.11 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.26), residues: 1070 helix: 1.63 (0.18), residues: 814 sheet: None (None), residues: 0 loop : -1.04 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 414 HIS 0.002 0.001 HIS A 135 PHE 0.016 0.001 PHE B 268 TYR 0.025 0.001 TYR A 282 ARG 0.002 0.000 ARG A 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.977 Fit side-chains REVERT: A 349 MET cc_start: 0.9388 (mmm) cc_final: 0.8982 (mmm) REVERT: A 540 MET cc_start: 0.8744 (ttp) cc_final: 0.8429 (ttm) REVERT: B 118 MET cc_start: 0.8890 (OUTLIER) cc_final: 0.8667 (ttm) REVERT: B 267 ASP cc_start: 0.8282 (t0) cc_final: 0.8025 (t0) outliers start: 10 outliers final: 6 residues processed: 77 average time/residue: 1.2609 time to fit residues: 103.8873 Evaluate side-chains 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 279 MET Chi-restraints excluded: chain A residue 323 ASP Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 118 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 4 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 75 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 65 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.066223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.050931 restraints weight = 27071.605| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.32 r_work: 0.2750 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8688 Z= 0.198 Angle : 0.545 13.074 11810 Z= 0.275 Chirality : 0.040 0.157 1376 Planarity : 0.004 0.044 1440 Dihedral : 7.478 111.798 1226 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.21 % Allowed : 12.89 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.25), residues: 1070 helix: 1.64 (0.18), residues: 814 sheet: None (None), residues: 0 loop : -1.04 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 414 HIS 0.003 0.001 HIS B 335 PHE 0.018 0.001 PHE B 251 TYR 0.025 0.001 TYR A 282 ARG 0.006 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.991 Fit side-chains REVERT: A 349 MET cc_start: 0.9373 (mmm) cc_final: 0.8936 (mmm) REVERT: A 540 MET cc_start: 0.8779 (ttp) cc_final: 0.8387 (ttm) REVERT: B 267 ASP cc_start: 0.8306 (t0) cc_final: 0.8058 (t0) REVERT: B 295 MET cc_start: 0.8757 (mtt) cc_final: 0.8461 (mtt) outliers start: 11 outliers final: 4 residues processed: 79 average time/residue: 1.4673 time to fit residues: 123.4514 Evaluate side-chains 75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 101 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 72 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 0.0470 chunk 85 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.067098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.051819 restraints weight = 27105.496| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 3.34 r_work: 0.2774 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8688 Z= 0.156 Angle : 0.538 14.354 11810 Z= 0.274 Chirality : 0.040 0.179 1376 Planarity : 0.005 0.045 1440 Dihedral : 7.326 104.713 1226 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.10 % Allowed : 12.89 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.25), residues: 1070 helix: 1.67 (0.18), residues: 810 sheet: None (None), residues: 0 loop : -1.08 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 414 HIS 0.002 0.001 HIS A 135 PHE 0.015 0.001 PHE B 251 TYR 0.025 0.001 TYR A 282 ARG 0.003 0.000 ARG B 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.978 Fit side-chains REVERT: A 241 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8532 (p) REVERT: A 349 MET cc_start: 0.9397 (mmm) cc_final: 0.8982 (mmm) REVERT: A 540 MET cc_start: 0.8752 (ttp) cc_final: 0.8374 (ttm) REVERT: B 267 ASP cc_start: 0.8337 (t0) cc_final: 0.8079 (t0) REVERT: B 272 MET cc_start: 0.9398 (ttm) cc_final: 0.9139 (mmm) outliers start: 10 outliers final: 4 residues processed: 78 average time/residue: 1.3834 time to fit residues: 115.9413 Evaluate side-chains 75 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 80 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 58 optimal weight: 0.0670 chunk 89 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 4 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.065974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.050684 restraints weight = 27071.189| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.30 r_work: 0.2746 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8688 Z= 0.215 Angle : 0.579 13.651 11810 Z= 0.288 Chirality : 0.041 0.167 1376 Planarity : 0.005 0.044 1440 Dihedral : 7.371 100.541 1226 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.88 % Allowed : 13.44 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.26), residues: 1070 helix: 1.63 (0.18), residues: 826 sheet: None (None), residues: 0 loop : -1.01 (0.37), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 414 HIS 0.003 0.001 HIS A 335 PHE 0.017 0.001 PHE A 251 TYR 0.023 0.001 TYR A 282 ARG 0.001 0.000 ARG A 394 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 69 time to evaluate : 1.059 Fit side-chains REVERT: A 99 MET cc_start: 0.9594 (mtm) cc_final: 0.9314 (mtp) REVERT: A 241 THR cc_start: 0.8956 (OUTLIER) cc_final: 0.8533 (p) REVERT: A 323 ASP cc_start: 0.9434 (t0) cc_final: 0.8904 (p0) REVERT: A 349 MET cc_start: 0.9392 (mmm) cc_final: 0.8957 (mmm) REVERT: B 267 ASP cc_start: 0.8349 (t0) cc_final: 0.8090 (t0) outliers start: 8 outliers final: 4 residues processed: 74 average time/residue: 1.3460 time to fit residues: 106.7633 Evaluate side-chains 74 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 322 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 3 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 0.0670 chunk 105 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 overall best weight: 0.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 372 ASN B 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.067627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.052293 restraints weight = 27118.483| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 3.37 r_work: 0.2777 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8688 Z= 0.153 Angle : 0.543 12.585 11810 Z= 0.274 Chirality : 0.040 0.157 1376 Planarity : 0.005 0.045 1440 Dihedral : 7.235 91.354 1226 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.77 % Allowed : 13.22 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.25), residues: 1070 helix: 1.65 (0.18), residues: 822 sheet: None (None), residues: 0 loop : -1.07 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 414 HIS 0.002 0.001 HIS A 135 PHE 0.015 0.001 PHE B 251 TYR 0.023 0.001 TYR A 282 ARG 0.001 0.000 ARG A 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4772.94 seconds wall clock time: 83 minutes 20.26 seconds (5000.26 seconds total)